Week 13, 14, 15 Virtual
All 4 libraries (1202 ligands) were screened along with 5 positive controls and 5 random controls for Listeria monocytogenes; none of the positive controls made it to the top 120. A random control made it to the top 60. All results were ranked, and the top 30 were submitted to Dr. B and put in my google student folder.
YopH enzyme and inhibition assays
YopH activity was measured via enzyme assays. As the amount of enzyme increased, the phosphatase activity also increased. There was no phosphatase activity whatsoever without enzyme.
Inhibition assays could not be carried out as the compounds dissolved in DMSO were prepared incorrectly (no compounds were added at all). This lead to 0 inhibition of the enzyme.
Week 11 & 12 Ligand Prep
Found positive and negative controls but could not get Maestro to function. Told to try again next week when Maestro may be working.
*This is a really intense ROTC week, I didn't get anything else done
SORRY I was dealing with my friend's death last night 9DEC13
Week 9 & 10 Nice job but could have more results for these couple of weeks. - BN Homology Model
The homology model was started but has not been completed; the Mycobacterium tuburculosis mPtpB protein structure will be used to construct the homology model.
Cloning attempt #2
Cloning was not succesful, after cohesive end generation and annealing, transformation failed as no colonies were present on the LB+agar+suc plates. This may be attributed to the previous low concentrations of PCR clean up and Midi Prep. More PCR product and pNIC-Bsa4 will be grown up in order for another attempt at cloning.
MidiPrep
The previously mentioned pNIC-Bsa4 cells were put through Midi prep to obtain pure plasmid. The concentration is, again, lower than desired, but there is an obvious increase and decrease in the slope of the concentration graph at 260nm. The plamid will be used for cloning.
Figure 1: Output of a 2ul sample of pNIC-Bsa4 plasmid after Midiprep in a nandrop spectrophotometer. The concentration is 22.6 ng/uL; the purities at 260/280 and 260/230 are 1.88 and 4.50 respectively.
Good work, captions under images could be better. -UM
Week 7 & 8 Transformation of competent cells for plasmid prep of pNIC-Bsa4
pNIC-Bsa4 cells were grown up again and spun down to produce 4 more pellets. They were frozen and stored and will be used for Midi prep in order to obtain pNIC-Bsa4 DNA.
PCR^2
*Something seems to be up with the new 100bp ladder; they run faster than other ladders and samples.
Figure 4: Agarose gel results of PCR^2. The first (leftmost) lane contains 100bp ladder. The second, third, fifth, and sixth lane contain 4 samples of PCR^2 mix (secondary PCR template, forward and reverse primers).
*Lane 4 was skipped due to well damage.
Figure 4: Agarose gel results of PCR^2. The first (leftmost) lane contains 100bp ladder. The second, third, fourth, and fifth contain 4 samples of PCR^2 mix (secondary PCR template, forward and reverse primers). The rightmost lane contained 1kb ladder.
*Faint bands and contamination in this run
Cloning
Cloning was not succesful, after cohesive end generation and annealing, transformation failed as no colonies were present on the LB+agar+suc plates. This may be attributed to the previous low concentrations of PCR clean up and Midi Prep. More PCR product and pNIC-Bsa4 will be grown up in order for another attempt at cloning.
Midi Prep The previously frozen pNIC-Bsa4 pellets had the DNA extracted. The average concentration of two samples after Midi prep came out to be 19.85 ng/ul; this value is extremely low. Thus, cloning will probably not be successful. The DNA sequencing results also did not match to any known genomes when run through BLAST comparisons. Too much DNA may have been lost during Midi prep.
Good job! What are the last 4 wells in figure 4? Keep up the world class research - Michael T.
Week 5 & 6 pNIC
Grown up overnight, centrifuged, and decanted.
After being left overnight, the LB media mixed with one colony of pNIC and antibiotic appeared cloudy and turbid. This was spun down resulting in 4 pellets which were then stored and frozen.
PyMOL Refresher
Completed.
PCR
PCR cleanup - Completed
Figure 4: Agarose gel results of PCR^2. The first (leftmost) lane contains 1kb ladder. The second, third, fourth, and 5th lane contain 4 samples of PCR^2 mix (secondary PCR template, forward and reverse primers).
The four samples produced one band per lane, thus PCR^2 was almost certainly successful. No contamination bands exist, though light smears appear to have formed above the bands.
Figure 3: Agarose gel results of failed PCR^2. The gel broken near the top of the gel. The leftmost lane contains 100bp ladder.
Figure 2: Agarose gel result of secondary PCR. First (leftmost) lane is a 100bp ladder. The second leftmost lane contains primary PCR template with the addition of forward and reverse primer for lmon PTP.
Secondary PCR was successful *(confirmed; PCR^2 succeeded) as evidenced by a single, highly concentrated (bright) band in the lane. There is a slight smear above the band, but the band in lane is overt and bright enough to say that secondary PCR was successful.
Figure 1: Agarose gel results for primary PCR. First (leftmost) lane is a 100bp ladder. Second lane is oligo mix after PCR for lmon PTP gene of interest.
Primary PCR was successful as there is a smear in the second lane. There seems to a be a high concentration, as shown by a bright band near the bottom of the smear, which may be oligos not joined together during PCR.
Primer dilution: Complete Primer dilution was successful as secondary PCR and PCR^2 were successful.
Week 3 & 4
James - very good page! - 092713 - Dr. B Restriction Enzyme Digest
Figure 1: Image of PCR of 1 kb DNA ladder in lane 1, uncut pGBR22 plasmid in lane 2, pGBR22 plasmid with EcoRI restriction enzyme in lane 3, pGBR22 plasmid with PvuII restriction enzyme in lane 4, pGBR22 plasmid with EcoRI and PvuII restriction enzymes in lane 5, and pGBR22 plasmid with no restriction enzymes in lane 6.
This RE digest, though not 100% perfect, worked just as it should. Lanes 2 and 6 had no EcoRI or PvuII and would not have been cut anywhere along the plasmid. The concentration of matter also appear in the same position and the correct position by size in lane. EcoRI would only have cut the plasmid once resulting in one band as in lane 3. PvuII cut the plasmid twice resulting in two bands as shown by lane 4. EcoRI and PvuII cut the plasmid 3 times resulting in three bands as seen in lane 5.
PCR Primer Design Tails
Forward Primer:5’ TACTTCCAATCCATGAAGAATTGGGTTAAA 3’ 30 bpGC Content 33.3% 0 mM Mg2+ Tm 57.2oC 1.5 mM Mg2+ Tm 65.1 oC 2 mM Mg2+ Tm 65.7oC 4 mM Mg2+ Tm 67.0 oC 6 mM Mg2+ Tm 67.5oC Reverse Primer:5’ AAAGCGTACCTGTACTAACAGTAAAGGTGGATA 3’ 33 bpReverse complement it: 5’ TATCCACCTTTACTGTTAGTACAGGTACGCTTT 3’ 33 bp0 mM Mg2+ Tm 60.4oC 1.5 mM Mg2+ Tm 68.0oC 2 mM Mg2+ Tm 68.5oC 4 mM Mg2+ Tm 69.6oC 6 mM Mg2+ Tm 70.1oC
GC Content 39.4%
Results from analysis of lmon PTP gene of interest.
Virtual predictions of how the BsaI enzyme will react with the insert and the full sequence along with virtual PCR images.
The gene of interest was analyzed and virtually inserted into the full pNIC-BSA4 sequence and virtually acquired (though not shown). This will hopefully occur in wet lab in order to clone the gene of interest.
Primary PCR
Figure 1: PCR image result of listeria monocytogenes oligo mix in lane 3 next to 100 bp ladder in lane 2.
The results of primary PCR for the GOI appears to have been successful except for the fact that the concentration (bright band) is near the bottom of the ladder when it should be next to the 900 bp marker on the ladder. This could be the result of oligos not coming together. Regardless, this template will be used for secondary PCR.
Week 1 & 2
James - good job. Crop your gel images to remove alot of the black. Dr. B 090913
PCR
Fig. 1: Results of putting one ladder and 4 samples of 1:1000, 1:1000, 1:100, and 0 DNA template mixed with taq dilutions, primer, and polymerase.
For the most part, the gel seems to have run successfully since a distinct band does appear in lanes 2-4 for samples A, B, and C, but not so much for lane 5, sample D, which had no DNA. What may be a light band in lane 5 may be due to contamination while loading the other lanes while preparing the gel.
Oligo Primer Design 22 oligonucleotides need to be synthesized ---------------------------------------------------------------- 1 ATGAAAAATTGGGTTAAAGTTACCGGTGCGGGTGTCCTGTCTGCA 45 2 CCTTCTCTTCAGACTGCGCACCGCAACCACCCAGCAGCAGGGTTGCAGACAGGACACCCG 60 3 GCGCAGTCTGAAGAGAAGGCCGAAGCGAACGTAAAAACCGAGCAGACCCTGAAACCGGGT 60 4 GAGGTCACGGACGTTTACCGCACCTTCCAGTTTGATCTGGCTACCCGGTTTCAGGGTCTG 60 5 GGTAAACGTCCGTGACCTCGGTGGCTACAAAACCACCGATGGTCTCACCATCAAACCGCA 60 6 TGTCAGACAGATTCGCCAGTTCCGCAGAACGGATCAGTTTGTGCGGTTTGATGGTGAGAC 60 7 CTGGCGAATCTGTCTGACAGCGACAAAAAGAAGCTGGTTAACACCTACGACCTGAGCCAC 60 8 CGGTTTGGTCGCAACTTCAGAAGACGTACGGAAGTCTACGATGTGGCTCAGGTCGTAGGT 60 9 TGAAGTTGCGACCAAACCGGACCCGAAACTGACCGACGTTGACTACACCCACGACTCTGT 60 10 TCAGGTCCTGGGTGCTCGTAGAGGTACCGTTGTCCTTCATAACAGAGTCGTGGGTGTAGT 60 11 GAGCACCCAGGACCTGACGGCGTCTCTGGCAAAAATGGACAACCCGGAAACCTTCCTGAT 60 12 GGATAGAAGTTTCGTCGGTGATGAAAGATTTGTTCGCGTTAATCAGGAAGGTTTCCGGGT 60 13 TCACCGACGAAACTTCTATCCAGGCGTACAAAGACTTCTTCGACATCCTGCTGGCCAACC 60 14 CGGTCTTTACCCGCGGTACAGTGCCACAGAACAGAACCGTCTTGGTTGGCCAGCAGGATG 60 15 ACCGCGGGTAAAGACCGTGCAGGTTTCGGCACGGCGCTCGTTCTCTCTGCGCTGGGCGTT 60 16 ATATTTGTTAGACAGCATGTAGTCGTCGATGACGGTGTTCTTGTCAACGCCCAGCGCAGA 60 17 CGACTACATGCTGTCTAACAAATATCGCGCTGACGAAAACAAGAAGGCGATCGAAGCAGT 60 18 GTCATACCGTCGATAACTTTTTTGTTGTCGGTCTTCGCTGCTACTGCTTCGATCGCCTTC 60 19 CAAAAAAGTTATCGACGGTATGACCGCCGTAATGGAAGTTCGTGAATCTTACATCAACGC 60 20 CCATGCTGCCGTACTTCGCATTAATCTCATCGAACGCTGCGTTGATGTAAGATTCACGAA 60 21 CGAAGTACGGCAGCATGGATAATTTCCTCAAAGAAAAACTGGGTCTGACGGACGCTAAAA 60 22 TTAGTACAGGTACGCTTTTTTCAGCTGCTCTTTTTTAGCGTCCGTCAGACC 51 Fig 1: Oligo primer sequences optimized for E. coli for the listeria monocytogenes EGD-e.
Oligo primers were successfully designed for the listeria monocytogenes EGD-e gene. These were optimized to be grown in E. coli and will be ordered in order to be used in expression of listeria monocytogenes EGD-e.
Week 1 Submitting to DNA sequencing core:
NNNNNNNNNNNNGGGNNNNNGGGCCCGACGTCGCATGCTCCCGGCCGCCATGGCCGCGGGNTTTTAGTGATGGTGATGGTGATGACCGAGCAAAGAGTGGCGTGCAATGGATATTTCACACTGCTCAACAAATGTGTAATCCTTGTTGTGACTGGTTACATCCAGTTTGCGGTCAACATAGTGATACCCTGGCATCCTCACAGGCTTCTTTGCCTTGTAAGTAGATTTGAATTCACACAAATAGTAACCACCTCCTTCCAACTTCAGAGCCATAAAGTTGTTTCCTATCAGCATTCCATCTCGTGCAAAGAGACGCTCAGTGTTGGGTTCCCAGCCCTGTGTCTTCTTCTGCATAACAGGTCCATTGGGAGGAAAGTTCACACCAGAGATTTTGACATTGTAGATGAAACAGTTGCCTTGGATGCTGGAATCATTGCTGACAGTACACACTGCACCATCTTCAAAGTTCATGATCCTCTCCCATGTATATCCCTCAGGGAATGACTGCTTTACATAATCAGGGATGTCTTCAGGGTACTTGGTGAATGGTATGCTTCCGTATTGAGACAGTGGTGATAAAATATCCCAAGCAAATGGCAGAGGTCCACCCTTGGTGACAGTGAGCTTTACCGTCTGCTCCCCCTCGTAAGGCTTTCCTTTTCCATCGCCTTCGACCTCAAAGTAGTGTCCATTGACCGTGCCTGACATATAAACCTTGTANGTCATTTGTTTAGCGATCACACTCATGATATTTCTCCTTCAATCAATCAAAATCACTAGTGCGGCCGCCTGCNNNCGACCATATGGGAGAGCTCCCAACGCGTTGGATGCATAGCTTGAGTATTCTATAGTGTCACCTAAATAGCTTGGNGTAATCATGGTCATAGCTGTTTCCTGTGTGAAATTGTTATCCGCTCACAATTCCACACAACATACGAGCCNGAAGCATAAAGTGTAAAGCCTGGNNNNCTAATGANNGAGCTACTCACATTNTNGCGTTGCGNTCNCNNCCGCTTTCNNTNGGAANCNGNNNNCNNCTGCNTNNNANNGNANNNNNNGGNANNGNGNNNNNNNTGGNNNNTNNNNNNNNNNNTNNNNNNNTNNNTGNNNNGNNNTNGNTGNGNNNNNNNNNNNNNNNNNNNNNNGNANNNNNNNNNCNNAANNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNNNNANGCCNNTNNNGGNNNTTNNNNNNANN Fig 1: The output for the DNA sequencing core for M13F primer for the DNA sequence of the primer witht he base pairs A, T, C, G. N represents base pairs that could not be determined with absolute certainty.
This particular order had to be run twice through DNA sequencing, however a sequence was obtained and did have comparable results to other organisms but not in the human genome.
Nanodrop:
Fig. 1: DNA template after being put through nanodrop spectrophotometer.
Fig 2: Second measurement of DNA put through nanodrop spectrophotometer.
The concentrations obtained from the nanodrop spectrophotometer were consistent, but both were not around 204.5 ng/uL which was the expected concentration. This may be due to the shelf life of the DNA or other environmental factors.
Virtual
All 4 libraries (1202 ligands) were screened along with 5 positive controls and 5 random controls for Listeria monocytogenes; none of the positive controls made it to the top 120. A random control made it to the top 60. All results were ranked, and the top 30 were submitted to Dr. B and put in my google student folder.
YopH enzyme and inhibition assays
YopH activity was measured via enzyme assays. As the amount of enzyme increased, the phosphatase activity also increased. There was no phosphatase activity whatsoever without enzyme.
Inhibition assays could not be carried out as the compounds dissolved in DMSO were prepared incorrectly (no compounds were added at all). This lead to 0 inhibition of the enzyme.
Week 11 & 12
Ligand Prep
Found positive and negative controls but could not get Maestro to function. Told to try again next week when Maestro may be working.
*This is a really intense ROTC week, I didn't get anything else done
SORRY I was dealing with my friend's death last night 9DEC13
Week 9 & 10
Nice job but could have more results for these couple of weeks. - BN
Homology Model
The homology model was started but has not been completed; the Mycobacterium tuburculosis mPtpB protein structure will be used to construct the homology model.
Cloning attempt #2
Cloning was not succesful, after cohesive end generation and annealing, transformation failed as no colonies were present on the LB+agar+suc plates. This may be attributed to the previous low concentrations of PCR clean up and Midi Prep. More PCR product and pNIC-Bsa4 will be grown up in order for another attempt at cloning.
Midi Prep
The previously mentioned pNIC-Bsa4 cells were put through Midi prep to obtain pure plasmid. The concentration is, again, lower than desired, but there is an obvious increase and decrease in the slope of the concentration graph at 260nm. The plamid will be used for cloning.
Good work, captions under images could be better. -UM
Week 7 & 8
Transformation of competent cells for plasmid prep of pNIC-Bsa4
pNIC-Bsa4 cells were grown up again and spun down to produce 4 more pellets. They were frozen and stored and will be used for Midi prep in order to obtain pNIC-Bsa4 DNA.
PCR^2
*Something seems to be up with the new 100bp ladder; they run faster than other ladders and samples.
*Lane 4 was skipped due to well damage.
*Faint bands and contamination in this run
Cloning
Cloning was not succesful, after cohesive end generation and annealing, transformation failed as no colonies were present on the LB+agar+suc plates. This may be attributed to the previous low concentrations of PCR clean up and Midi Prep. More PCR product and pNIC-Bsa4 will be grown up in order for another attempt at cloning.
Midi Prep
The previously frozen pNIC-Bsa4 pellets had the DNA extracted. The average concentration of two samples after Midi prep came out to be 19.85 ng/ul; this value is extremely low. Thus, cloning will probably not be successful. The DNA sequencing results also did not match to any known genomes when run through BLAST comparisons. Too much DNA may have been lost during Midi prep.
Good job! What are the last 4 wells in figure 4? Keep up the world class research - Michael T.
Week 5 & 6
pNIC
Grown up overnight, centrifuged, and decanted.
After being left overnight, the LB media mixed with one colony of pNIC and antibiotic appeared cloudy and turbid. This was spun down resulting in 4 pellets which were then stored and frozen.
PyMOL Refresher
Completed.
PCR
PCR cleanup - Completed
The four samples produced one band per lane, thus PCR^2 was almost certainly successful. No contamination bands exist, though light smears appear to have formed above the bands.
Secondary PCR was successful *(confirmed; PCR^2 succeeded) as evidenced by a single, highly concentrated (bright) band in the lane. There is a slight smear above the band, but the band in lane is overt and bright enough to say that secondary PCR was successful.
Primary PCR was successful as there is a smear in the second lane. There seems to a be a high concentration, as shown by a bright band near the bottom of the smear, which may be oligos not joined together during PCR.
Primer dilution: Complete
Primer dilution was successful as secondary PCR and PCR^2 were successful.
Week 3 & 4
James - very good page! - 092713 - Dr. B
Restriction Enzyme Digest
This RE digest, though not 100% perfect, worked just as it should. Lanes 2 and 6 had no EcoRI or PvuII and would not have been cut anywhere along the plasmid. The concentration of matter also appear in the same position and the correct position by size in lane. EcoRI would only have cut the plasmid once resulting in one band as in lane 3. PvuII cut the plasmid twice resulting in two bands as shown by lane 4. EcoRI and PvuII cut the plasmid 3 times resulting in three bands as seen in lane 5.
PCR Primer Design Tails
Forward Primer:5’ TACTTCCAATCCATGAAGAATTGGGTTAAA 3’ 30 bpGC Content 33.3% 0 mM Mg2+ Tm 57.2oC 1.5 mM Mg2+ Tm 65.1 oC 2 mM Mg2+ Tm 65.7oC 4 mM Mg2+ Tm 67.0 oC 6 mM Mg2+ Tm 67.5oC Reverse Primer:5’ AAAGCGTACCTGTACTAACAGTAAAGGTGGATA 3’ 33 bpReverse complement it: 5’ TATCCACCTTTACTGTTAGTACAGGTACGCTTT 3’ 33 bp0 mM Mg2+ Tm 60.4oC 1.5 mM Mg2+ Tm 68.0oC 2 mM Mg2+ Tm 68.5oC 4 mM Mg2+ Tm 69.6oC 6 mM Mg2+ Tm 70.1oC
GC Content 39.4%
Results from analysis of lmon PTP gene of interest.
Virtual predictions of how the BsaI enzyme will react with the insert and the full sequence along with virtual PCR images.
The gene of interest was analyzed and virtually inserted into the full pNIC-BSA4 sequence and virtually acquired (though not shown). This will hopefully occur in wet lab in order to clone the gene of interest.
Primary PCR
The results of primary PCR for the GOI appears to have been successful except for the fact that the concentration (bright band) is near the bottom of the ladder when it should be next to the 900 bp marker on the ladder. This could be the result of oligos not coming together. Regardless, this template will be used for secondary PCR.
Week 1 & 2
James - good job. Crop your gel images to remove alot of the black. Dr. B 090913
PCR
For the most part, the gel seems to have run successfully since a distinct band does appear in lanes 2-4 for samples A, B, and C, but not so much for lane 5, sample D, which had no DNA. What may be a light band in lane 5 may be due to contamination while loading the other lanes while preparing the gel.
Oligo Primer Design
22 oligonucleotides need to be synthesized
----------------------------------------------------------------
1 ATGAAAAATTGGGTTAAAGTTACCGGTGCGGGTGTCCTGTCTGCA 45
2 CCTTCTCTTCAGACTGCGCACCGCAACCACCCAGCAGCAGGGTTGCAGACAGGACACCCG 60
3 GCGCAGTCTGAAGAGAAGGCCGAAGCGAACGTAAAAACCGAGCAGACCCTGAAACCGGGT 60
4 GAGGTCACGGACGTTTACCGCACCTTCCAGTTTGATCTGGCTACCCGGTTTCAGGGTCTG 60
5 GGTAAACGTCCGTGACCTCGGTGGCTACAAAACCACCGATGGTCTCACCATCAAACCGCA 60
6 TGTCAGACAGATTCGCCAGTTCCGCAGAACGGATCAGTTTGTGCGGTTTGATGGTGAGAC 60
7 CTGGCGAATCTGTCTGACAGCGACAAAAAGAAGCTGGTTAACACCTACGACCTGAGCCAC 60
8 CGGTTTGGTCGCAACTTCAGAAGACGTACGGAAGTCTACGATGTGGCTCAGGTCGTAGGT 60
9 TGAAGTTGCGACCAAACCGGACCCGAAACTGACCGACGTTGACTACACCCACGACTCTGT 60
10 TCAGGTCCTGGGTGCTCGTAGAGGTACCGTTGTCCTTCATAACAGAGTCGTGGGTGTAGT 60
11 GAGCACCCAGGACCTGACGGCGTCTCTGGCAAAAATGGACAACCCGGAAACCTTCCTGAT 60
12 GGATAGAAGTTTCGTCGGTGATGAAAGATTTGTTCGCGTTAATCAGGAAGGTTTCCGGGT 60
13 TCACCGACGAAACTTCTATCCAGGCGTACAAAGACTTCTTCGACATCCTGCTGGCCAACC 60
14 CGGTCTTTACCCGCGGTACAGTGCCACAGAACAGAACCGTCTTGGTTGGCCAGCAGGATG 60
15 ACCGCGGGTAAAGACCGTGCAGGTTTCGGCACGGCGCTCGTTCTCTCTGCGCTGGGCGTT 60
16 ATATTTGTTAGACAGCATGTAGTCGTCGATGACGGTGTTCTTGTCAACGCCCAGCGCAGA 60
17 CGACTACATGCTGTCTAACAAATATCGCGCTGACGAAAACAAGAAGGCGATCGAAGCAGT 60
18 GTCATACCGTCGATAACTTTTTTGTTGTCGGTCTTCGCTGCTACTGCTTCGATCGCCTTC 60
19 CAAAAAAGTTATCGACGGTATGACCGCCGTAATGGAAGTTCGTGAATCTTACATCAACGC 60
20 CCATGCTGCCGTACTTCGCATTAATCTCATCGAACGCTGCGTTGATGTAAGATTCACGAA 60
21 CGAAGTACGGCAGCATGGATAATTTCCTCAAAGAAAAACTGGGTCTGACGGACGCTAAAA 60
22 TTAGTACAGGTACGCTTTTTTCAGCTGCTCTTTTTTAGCGTCCGTCAGACC 51
Fig 1: Oligo primer sequences optimized for E. coli for the listeria monocytogenes EGD-e.
Oligo primers were successfully designed for the listeria monocytogenes EGD-e gene. These were optimized to be grown in E. coli and will be ordered in order to be used in expression of listeria monocytogenes EGD-e.
Week 1
Submitting to DNA sequencing core:
NNNNNNNNNNNNGGGNNNNNGGGCCCGACGTCGCATGCTCCCGGCCGCCATGGCCGCGGGNTTTTAGTGATGGTGATGGTGATGACCGAGCAAAGAGTGGCGTGCAATGGATATTTCACACTGCTCAACAAATGTGTAATCCTTGTTGTGACTGGTTACATCCAGTTTGCGGTCAACATAGTGATACCCTGGCATCCTCACAGGCTTCTTTGCCTTGTAAGTAGATTTGAATTCACACAAATAGTAACCACCTCCTTCCAACTTCAGAGCCATAAAGTTGTTTCCTATCAGCATTCCATCTCGTGCAAAGAGACGCTCAGTGTTGGGTTCCCAGCCCTGTGTCTTCTTCTGCATAACAGGTCCATTGGGAGGAAAGTTCACACCAGAGATTTTGACATTGTAGATGAAACAGTTGCCTTGGATGCTGGAATCATTGCTGACAGTACACACTGCACCATCTTCAAAGTTCATGATCCTCTCCCATGTATATCCCTCAGGGAATGACTGCTTTACATAATCAGGGATGTCTTCAGGGTACTTGGTGAATGGTATGCTTCCGTATTGAGACAGTGGTGATAAAATATCCCAAGCAAATGGCAGAGGTCCACCCTTGGTGACAGTGAGCTTTACCGTCTGCTCCCCCTCGTAAGGCTTTCCTTTTCCATCGCCTTCGACCTCAAAGTAGTGTCCATTGACCGTGCCTGACATATAAACCTTGTANGTCATTTGTTTAGCGATCACACTCATGATATTTCTCCTTCAATCAATCAAAATCACTAGTGCGGCCGCCTGCNNNCGACCATATGGGAGAGCTCCCAACGCGTTGGATGCATAGCTTGAGTATTCTATAGTGTCACCTAAATAGCTTGGNGTAATCATGGTCATAGCTGTTTCCTGTGTGAAATTGTTATCCGCTCACAATTCCACACAACATACGAGCCNGAAGCATAAAGTGTAAAGCCTGGNNNNCTAATGANNGAGCTACTCACATTNTNGCGTTGCGNTCNCNNCCGCTTTCNNTNGGAANCNGNNNNCNNCTGCNTNNNANNGNANNNNNNGGNANNGNGNNNNNNNTGGNNNNTNNNNNNNNNNNTNNNNNNNTNNNTGNNNNGNNNTNGNTGNGNNNNNNNNNNNNNNNNNNNNNNGNANNNNNNNNNCNNAANNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNNNNANGCCNNTNNNGGNNNTTNNNNNNANN
Fig 1: The output for the DNA sequencing core for M13F primer for the DNA sequence of the primer witht he base pairs A, T, C, G. N represents base pairs that could not be determined with absolute certainty.
This particular order had to be run twice through DNA sequencing, however a sequence was obtained and did have comparable results to other organisms but not in the human genome.
Nanodrop:
The concentrations obtained from the nanodrop spectrophotometer were consistent, but both were not around 204.5 ng/uL which was the expected concentration. This may be due to the shelf life of the DNA or other environmental factors.